Mapping functional zones for rural landscapes is the foundational work for rural land use planning and plays a very important role in the economic development and resource management utilization of rural areas. However, the traditional manual delineation of functional zone boundaries empirically in rural areas is labor-intensive, time-consuming, and lacks the consideration of spatial landscape patterns. The emergence of high-resolution remote sensing imagery and image segmentation has facilitated the analysis of ground landscape information and patterns, but there is still a lack of functional zone boundary mapping methods applicable to rural landscapes. To address this, we propose a functional zoning method called multiscale merging of landscape contextual and shape characteristics with heterogeneity indices (M2LHI) for mapping geographic boundaries for rural landscapes based on high-resolution remote sensing imagery. The landscape contextual features were first constructed based on the geospatial distances of landscape types, and then, the dominance index and shape index were introduced to quantify the landscape heterogeneity by object-oriented image analysis. Then, the automated merging of adjacent landscape units based on the thresholds of the landscape heterogeneity indices was performed to map the initial zones. The final rural functional zones were defined based on the main function in the zone. The study was carried out in three typical rural landscapes (hilly countryside, flat countryside, and grassland countryside) located in Fujian, Xinjiang, and Inner Mongolia, China, and the freely available Gaofen-2 (GF-2) satellite imagery was used as the data source. We compared the boundaries of mapped functional zones and reference functional zones, and the matching and inclusion ratios of the final functional zones mapped in each case were bigger than 78%, indicating that the M2LHI method has a high ability to map the functional spatial patterns. The overall accuracies of mapping functional zones with different functions were 95.9%, 89.0%, and 92.1% for the respective cases. The results demonstrated that the M2LHI method effectively quantifies landscape heterogeneity and accurately delineates functional zones with different landscape patterns. It can provide a scientific basis for rural planning and management and efficiently draw reasonable geographic boundaries for rural functional zones.